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LECTURE NO. 1
INSTRUCTOR ; DR. SAIMA HANIF
COURSE; BIOCHEMISTRY-I
SEPTEMBER 28, 2020 (MONDAY)

Department of Biological Sciences (DBS)

National University of Medical Sciences (NUMS)
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BIOCHEMISTRY…
The Chemistry of Life
 Learning outcomes
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 Introduction to Biochemistry.
 The Foundations of Biochemistry:

1. Cellular Foundation
2. Chemical Foundation
3. Physical Foundation
4. Genetic foundation
5. Evolutionary Foundation
 Bio Chemistry
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 Bio= life
 Chemistry = how things interact
 Biochemistry= the branch of science in which you
study the chemical and physical processes that
occur in an organism.
 1. Cellular Foundations
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 The unity and diversity of organisms become apparent

even at the cellular level. The smallest organisms
consist of single cells and are microscopic. Larger,
multicellular organisms contain many different types of
cells, which vary in size, shape, and specialized
function. Despite these obvious differences, all cells of
the simplest and most complex organisms share certain
fundamental properties, which can be seen at the
biochemical level.
  Cells Are the Structural and Functional Units
of All Living Organisms
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  Cellular Dimensions Are Limited by Diffusion
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 Most cells are microscopic, invisible to the unaided

eye. Animal and plant cells are typically 5 to 100
μm in diameter, and many unicellular
microorganisms are only 1 to 2 μm long
 The lower limit is probably set by the minimum
number of each type of biomolecule required by
the cell. The smallest cells, certain bacteria known
 as mycoplasmas, are 300 nm in diameter and have
a volume of about 10−14 mL.
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 The upper limit of cell size is probably set by the rate of

diffusion of solute molecules in aqueous systems. For
example, a bacterial cell that depends on oxygen-
consuming reactions for energy extraction must obtain
molecular oxygen by diffusion from the surrounding
medium through its plasma membrane.
  Organisms Belong to Three Distinct Domains
of Life
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Phylogeny of the three domains of life.

  Organisms Differ Widely in Their Sources of
Energy and Biosynthetic Precursors
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All organisms can be

classified according to
their source of energy
(sunlight or oxidizable
chemical compounds)
and their source of
carbon for the
synthesis of cellular
material.
  Bacterial and Archaeal Cells Share Common
Features but Differ in Important Ways
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 Eukaryotic Cells Have a Variety of Membranous
Organelles, Which Can Be Isolated for Study
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  Cells Build Supramolecular Structures
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 Summary
1.Cellular foundations
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 All cells are bounded by a plasma membrane; have a cytosol

containing metabolites, coenzymes, inorganic ions, and enzymes;
and have a set of genes contained within a nucleoid (bacteria and
archaea) or nucleus (eukaryotes).
 All organisms require a source of energy to perform cellular
work. Phototrophs obtain energy from sunlight; chemotrophs
obtain energy from chemical fuels, oxidizing the fuel and passing
electrons to good electron acceptors: inorganic compounds,
organic compounds, or molecular oxygen.
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 Bacterial and archaeal cells contain cytosol, a nucleoid, and

plasmids, all within a cell envelope. Eukaryotic cells have a
nucleus and are multicompartmented, with certain processes
segregated in specific organelles; organelles can be separated
and studied in isolation.
 Cytoskeletal proteins assemble into long filaments that give
cells shape and rigidity and serve as rails along which cellular
organelles move throughout the cell.
 Supramolecular complexes held together by noncovalent
interactions are part of a hierarchy of structures, some visible
with the light microscope. When individual molecules are
removed from these complexes to be studied in vitro,
interactions important in the living cell may be lost.
 2. Chemical Foundations
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 Nature is predominantly made of four elements: Hydrogen

(H), Oxygen (O), Nitrogen (N), and Carbon (C). Together they
make up over 99% of all living cells. These elements are the
lightest atoms that are capable of making up to four stable
and strong bonds. There are other elements that are also
essential to living organisms such as Sodium (Na), Potassium
(K), Calcium (Ca), and Sulfur (S). These are called trace
elements and usually are needed to help specific proteins to
function.
 All living cells have the common molecules of amino acids,
carbohydrates, lipids, and nucleic acids which all perform the
same functions in every cell.
  Biomolecules Are Compounds of Carbon with
a variety of Functional Groups
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 The chemistry of living organisms is organized around carbon,

which accounts for more than half of the dry weight of cells.
Carbon can form single bonds with hydrogen atoms, and both
single and double bonds with oxygen and nitrogen atoms . Of
greatest significance in biology is the ability of carbon atoms
to form very stable single bonds with up to four other carbon
atoms. Two carbon atoms also can share two (or three)
electron pairs, thus forming double (or triple) bonds.
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Fig. Bulk elements (shaded light red) are structural components of

cells and tissues and are required in the diet in gram quantities daily.
For trace elements (shaded yellow), the requirements are much
smaller: for humans, a few milligrams per day of Fe, Cu, and Zn, even
less of the others.
  Cells Contain a Universal Set of Small Molecules
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 Dissolved in the aqueous phase (cytosol) of all cells is a

collection of perhaps a thousand different small organic
molecules (Mr ∼100 to ∼500), with intracellular
concentrations ranging from nanomolar to millimolar .These
are the central metabolites in the major pathways occurring
in nearly every cell—the metabolites and pathways that have
been conserved throughout the course of evolution. This
collection of molecules includes the common amino acids,
nucleotides, sugars and their phosphorylated derivatives, and
mono-, di-, and tricarboxylic acids.
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 Secondary metabolites. There are other small biomolecules, specific to

certain types of cells or organisms. For example, vascular plants contain,
in addition to the universal set, small molecules called secondary
metabolites, which play roles specific to plant life. These metabolites
include compounds that give plants their characteristic scents and colors,
and compounds such as morphine, quinine, nicotine, and caffeine that
are valued for their physiological effects on humans but have other
purposes in plants.
 Metabolome The entire collection of small molecules in a given cell under
a specific set of conditions has been called the metabolome, in parallel
with the term “genome.” Metabolomics is the systematic characterization
of the metabolome under very specific conditions (such as following
administration of a drug or a biological signal such as insulin).
 Macromolecules Are the Major Constituents of
Cells
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 Carbohydrates…
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 Known as sugars and starches

 Also include cellulose and glycogen
 Made up of monosaccharides (monomer) which
can be put together to form disaccharides and
polysaccharides
 Disaccharides – sucrose (table sugar)
 Polysaccharides – starch, cellulose (cell wall
component), and glycogen (storage of carbs in the
liver and muscle)
 Glycogen is important for insulin in humans
 Why carbs are important to living organisms…
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 Short-term storage energy storage

 Plant cell wall components – strength
 Component of cell membranes – glycogen
 It helps identify the type of cell
 Proteins…
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 Known as meat to us
 Made up of amino acids (monomer) which can be
put together to form polypeptides (50-300 a.a.)
 20 different amino acids are found in human proteins
 Why proteins are important to living organism…
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 Form body tissue

 Skin, hair, muscles
 Important for immune response
 Antibodies – fight off foreign invaders
 All enzymes in the body
 Biological catalysts – they speed chemical reactions
inside the body
 Lipids…
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 Known as fats, oils and waxes

 Made up of glycerol and fatty acids
 Saturated fatty acids
 Single bonds join carbon (carbon – carbon) together
 Are oils at room temperatures

 Unsaturated fatty acids

 Has at least one carbon = carbon (joined by double bonds)
 3 fatty acids + 1 glycerol = triglyceride
 Why lipids are important to living organisms…
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 Long term storage of energy

 Fat is the storage mechanism
 Formation of cell membranes
 Nervesand brain tissue
 Phospholipids and cholesterol
 Phospholipids have hydrophobic heads and hydrophilic
tails
 Hormones
 Made of steroids
 Nucleic Acids…
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 Known as DNA and RNA

 Made up of nucleotides
A nucleotide consists of
 Phosphate group
 Pentose sugar (5-carbon sugar)
 Nitrogen base (A, T, C, G, or U)
 Why nucleic acids are important to living
things…
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 DNA
 Blueprintfor life
 Our genes

 RNA
 Translates DNA to make PROTEINS
  Three-Dimensional Structure Is Described by
Configuration and Conformation
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 Molecular configuration can be changed only by breaking

covalent bonds. For a carbon atom with four different
substituents (a chiral carbon), the substituent groups can be
arranged in two different ways, generating stereoisomers
with distinct properties. Only one stereoisomer is biologically
active. Molecular conformation is the position of atoms in
space that can be changed by rotation about single bonds,
without breaking covalent bonds.
 Configuration is conferred by the presence of either (1)
double bonds, around which there is little or no freedom of
rotation, or (2) chiral centers, around which substituent
groups are arranged in a specific orientation.
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Representations of molecules. Three ways to represent the structure of

the amino acid alanine (shown here in the ionic form found at neutral pH).
(a) Structural formula in perspective form: a solid wedge represents a bond
in which the atom at the wide end projects out of the plane of the paper,
toward the reader; a dashed wedge represents a bond extending behind
the plane of the paper. (b) Ball-and-stick model, showing bond angles and
relative bond lengths. (c) Space-filling model, in which each atom is shown
with its correct relative van der Waals radius.
  Interactions between Biomolecules Are
Stereospecific
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 When biomolecules interact, the “fit” between them must be

stereochemically correct. The three-dimensional structure of
biomolecules large and small— the combination of
configuration and conformation—is of the utmost importance
in their biological interactions: reactant with its enzyme,
hormone with its receptor on a cell surface, antigen with its
specific antibody,
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Fig. Complementary fit between a macromolecule and a

small molecule. A glucose molecule fits into a pocket on the
surface of the enzyme hexokinase and is held in this
orientation by several noncovalent interactions between the
protein and the sugar.
 Summary
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2. Chemical Foundations
 Because of its bonding versatility, carbon can produce a
broad array of carbon–carbon skeletons with a variety of
functional groups; these groups give biomolecules their
biological and chemical personalities.
 ■ A nearly universal set of about a thousand small molecules
is found in living cells; the interconversions of these
molecules in the central metabolic pathways have been
conserved in evolution.
 ■ Proteins and nucleic acids are linear polymers of simple
monomeric subunits; their sequences contain the
information that gives each molecule its three-dimensional
structure and its biological functions.
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 ■ Molecular configuration can be changed only by breaking

covalent bonds.For a carbon atom with four different
substituents (a chiral carbon), the substituent groups can be
arranged in two different ways, generating stereoisomers
with distinct properties. Only one stereoisomer is biologically
active. Molecular conformation is the position of atoms in
space that can be changed by rotation about single bonds,
without breaking covalent bonds.
 ■ Interactions between biological molecules are almost
invariably stereospecific: they require a close fit between
complementary structures in the interacting molecules.